diff --git a/align.c b/align.c
index b22a3f2..cd28d6a 100644
--- a/align.c
+++ b/align.c
@@ -563,11 +563,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 		re = (int32_t)a[as1+cnt1-1].x + 1;
 		qe = (int32_t)a[as1+cnt1-1].y + 1;
 	} else {
-		if (is_splice) {
-			mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
-		} else {
-			mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
-		}
+		if (!(opt->flag & MM_F_NO_END_FLT)) {
+			if (is_splice)
+				mm_fix_bad_ends_splice(km, opt, mi, r, mat, qlen, qseq0, a, &as1, &cnt1);
+			else
+				mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
+		} else as1 = r->as, cnt1 = r->cnt;
 		mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
 		mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30, opt->max_gap>>1);
 		mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
diff --git a/main.c b/main.c
index 87540ea..079155c 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "getopt.h"
 #endif
 
-#define MM_VERSION "2.11-r821-dirty"
+#define MM_VERSION "2.11-r822-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -62,6 +62,7 @@ static struct option long_options[] = {
 	{ "eqx",            no_argument,       0, 0 },   // 32
 	{ "paf-no-hit",     no_argument,       0, 0 },   // 33
 	{ "split-prefix",   required_argument, 0, 0 },   // 34
+	{ "no-end-flt",     no_argument,       0, 0 },   // 35
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -183,6 +184,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
 		else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
 		else if (c == 0 && long_idx ==34) opt.split_prefix = optarg; // --split-prefix
+		else if (c == 0 && long_idx ==35) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
 		else if (c == 0 && long_idx == 14) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
 		} else if (c == 0 && long_idx == 15) { // --secondary
diff --git a/minimap.h b/minimap.h
index 40a5d25..27ba911 100644
--- a/minimap.h
+++ b/minimap.h
@@ -33,6 +33,7 @@
 #define MM_F_COPY_COMMENT  0x2000000
 #define MM_F_EQX           0x4000000 // use =/X instead of M
 #define MM_F_PAF_NO_HIT    0x8000000 // output unmapped reads to PAF
+#define MM_F_NO_END_FLT    0x10000000
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2
diff --git a/minimap2.1 b/minimap2.1
index ced6c8c..bd67591 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -360,6 +360,10 @@ the length of the terminal gap in the chain. This option is only effective
 with
 .BR --splice .
 It helps to avoid tiny terminal exons. [6]
+.TP
+.B --no-end-flt
+Don't filter seeds towards the ends of chains before performing base-level
+alignment.
 .SS Input/output options
 .TP 10
 .B -a